can turn off ignore frag now

[jalview.git] / forester / ruby / evoruby / exe / run_phylo_pipeline.rb

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
index 163def7..5cd0401 100755 (executable)
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
@@ -14,17 +14,16 @@ module Evoruby
 
   class RunPhyloPipeline
 
-    PFAM      = "/home/czmasek/DATA/PFAM/PFAM260X/"
+    PFAM      = "/home/czmasek/DATA/PFAM/PFAM270X/"
     HMMSCAN  = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
     HSP       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
     D2F       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
     DSX       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
 
-
     def run
       unless ARGV.length >= 4 && ARGV.length <= 6
         error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> " +
-         "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias]"
+         "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias, --max for no heuristics]"
       end
 
       input       = ARGV[ 0 ]
@@ -54,6 +53,7 @@ module Evoruby
 
       base_name = get_base_name input
 
+      puts
       puts "1. hmmscan:"
       cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
       run_command( cmd )
@@ -70,7 +70,7 @@ module Evoruby
       puts
 
       puts "4. dsx:"
-      cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{base_name}_#{hmm}_ee#{e_value_exp.to_s}_#{length}"
+      cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{base_name}__#{hmm}__ee#{e_value_exp.to_s}_#{length}"
       run_command( cmd )
       puts